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Introduction to Molecular Physics:

Molecular physics is principally the study of the physical properties of molecules; the chemical bonds between atoms same as the molecular dynamics. It is most important experimental methods are various types of spectroscopy. The field is relatively close to atomic physics and overlaps greatly with theoretical/ hypothetical chemistry, physical chemistry and chemical physics.

In addition to the electronic excitation states which are known from atoms, molecules are able to vibrate and to rotate. These vibrations and rotations are quantized; there are discrete levels of energy. The minimum energy differences exist between different rotational states, so, pure rotational spectra are in the far infrared area (about 30 - 150 µm wavelength) of the electromagnetic spectrum. Vibrational spectra are in the about infrared (about 1 - 5 µm) and spectra resulting from electronic transitions are mainly in the visible and ultraviolet areas. From measuring rotational and vibrational spectra properties of molecules similar to the distance between the nuclei can be calculated.

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A molecular Double-Slit

One of the important aspects of molecular physics is that the essential atomic orbital theory in the field of atomic physics expands to the theory of molecular orbital.

Molecular Modeling

All hypothetical techniques and computational methods used to model or imitate the behavior of molecules are encompasses in molecular modeling. These techniques are used in the fields of drug design, computational chemistry, computational biology and materials science for research about the molecular systems which are ranging from petite chemical systems to huge biological molecules and material groups. The easiest computations can be executed by using the hands, but certainly computers are necessary to execute molecular modeling of any logically sized system. The most familiar feature of molecular modeling techniques is the atomistic level explanation of the molecular systems. Which include explicitly modeling electrons of each atom (the quantum chemistry approach), or treating atoms as the smallest individual unit (the Molecular mechanics approach).

Molecular Mechanics:

Molecular mechanics is one of the aspects of molecular modeling, as it refers to make use of classical mechanics/Newtonian mechanics to illustrate the physical foundation after the models. Molecular models generally describe atoms (nucleus and electrons together) as point charges with a connected mass. The connections among neighboring atoms are described by spring-like interactions (representing chemical bonds) and Vander Waals forces. The Lennard-Jones potential is usually used to describe van der Waals forces. The electrostatic connections are calculated based on Coulomb's law. Atoms are allocating to coordinates in Cartesian space or in internal coordinates and can also assign velocities in dynamical simulations. The atomic velocities can be associated to the temperature of the arrangement, a macroscopic quantity. The combined mathematical expression is called potential function and it is related to the system internal energy (U), a thermodynamic amount is equal to the addition of potential and kinetic energies. Techniques which reduce the potential energy are called energy minimization methods (e.g., steepest descent and conjugate gradient), while techniques that model the behavior of the system with propagation of time are called molecular dynamics.

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This function known as  a potential function, which calculates the molecular potential energy as an addition of energy terms that explains the difference of bond angles ,bond lengths and torsion angles away from equilibrium values, plus conditions for non-bonded pairs of atoms which describes van der Waals and electrostatic interactions. The set of parameters which are consisting of equilibrium bond lengths, bond angles, force constants partial charge values, and van der Waals parameters are collectively well-known as a force field. Unusual implementations of molecular mechanics use diverse mathematical expressions and dissimilar factors for the potential function. The commonly used force fields which are in use today have been invented by using high level quantum computations and/or fitting to experimental data. The method known as energy minimization is used to find positions of zero gradients for all atoms, other than this, a local energy minimum. Lower energy states are more constant and are commonly examined because of their role in chemical and biological procedures. A molecular dynamics simulation, alternatively, computes the behavior of a system as a function of time. It get involves solving Newton's laws of motion, primarily the 2nd law, F = ma. Integration of Newton's laws of motion, which makes use of using different integration algorithms, leads to atomic trajectories in time and space.  The force on an atom is described as the negative gradient of the potential energy function. The energy minimization method is helpful for getting a static picture for comparing among states of same systems, whilst molecular dynamics gives information about the dynamic procedures with the intrinsic inclusion of temperature effects.

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